plotabif: Electrophoregram plot for ABIF data

In seqinr: Biological Sequences Retrieval and Analysis

Electrophoregram plot for ABIF data

Description

Simple chromatogram plot for data imported with the read.abif function.

Usage

plotabif(abifdata, 
  chanel = 1, 
  tmin = 1/tscale, 
  tmax = abifdata$Data[["SCAN.1"]]/tscale, 
  tscale = 1000, 
  yscale = 1000, type = "l", las = 1, 
  xlab = paste("Time", tscale, sep = "/"),
  ylab = paste("RFU", yscale, sep = "/"), 
  irange = (tmin*tscale):(tmax*tscale),
  x = irange/tscale,
  xlim = c(tmin, tmax),
  chanel.names = c(1:4,105),
  DATA = paste("DATA", chanel.names[chanel], sep = "."),
  y = abifdata$Data[[DATA]][irange]/yscale,
  ylim = c(min(y), max(y)),
  dyn = abifdata$Data[[paste("DyeN", chanel, sep = ".")]],
  main = paste(deparse(substitute(abifdata)), chanel, dyn, sep = " ; "),
  calibr = NULL,
  ladder.bp = NULL,
  allele.names = "identifiler",
  ladder.lab = TRUE,
  ...)

Arguments

abifdata	the result returned by read.abif
chanel	the dye number
tmin	scaled starting time for the time axis
tmax	scaled ending time for the time axis
tscale	scale factor for the time axis
yscale	scale factor for the y-axis (RFU)
type	type of line drawing forwarded to plot
las	orientation of axis labels forwarded to plot
xlab	x-axis label forwarded to plot
ylab	y-axis label forwarded to plot
irange	indices of data to be plotted
x	values used for the x-axis
xlim	limits for the x-axis forwarded to plot
chanel.names	numbers extensions used for the DATA
DATA	names of the DATA components
y	values used for the y-axis
ylim	limits for the y-axis forwarded to plot
dyn	dye name
main	title for the plot forwarded to plot
calibr	an optional calibration function to convert time into bp
ladder.bp	an optional ladder scale in bp (calibr must be provided)
allele.names	name of the dataset with allele names
ladder.lab	logical: should allele names be added on plot
...	arguments forwarded to plot

Value

Returns invisibly its local graphical parameter settings.

Author(s)

J.R. Lobry

References

citation("seqinr")

See Also

function read.abif to import files in ABIF format, data gs500liz for internal size standards, data identifiler for allele names in the allelic ladder, data JLO for an example of an individual sample file, data ECH for an example of an allelic lader.

Examples

data(ECH)
plotabif(ECH,chanel = 1, tmin = 3.2, tmax = 6.1)

seqinr documentation built on March 31, 2023, 3:05 p.m.